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Diving into the Realm of Quantum Simulation

     Nanoparticles, quantum mechanics, molecular dynamics, supercomputers, and machine learning. All five of these topics sound like things that Tony Stark and Bruce Banner work on in their free time. However, with modern advances in computing technology these fields are actually able to exist and coexist in a beautiful way giving rise to the real-life field of nanomedicine. 

   I’m coming into the Reker lab as a rising sophomore BME student still trying to figure out what I actually want to study. My interests are spread over multiple disciplines, and it’s hard to pin down exactly one thing that I like. Growing up I loved playing with computers. Not building them like Jimmy Neutron, but simply playing video games like Minecraft. I loved how the computer was able to generate an environment that had similar rules to reality. You have objects in the world, collision rules, like when you jump on slime blocks, gravity, and a day-night cycle. Each of these parts of the simulation combine in a unique way to create the “world” and give a fun experience while playing the game. The combining of multiple processes to generate a real-life simulation is basically what Dr. Reker and other computational chemists are doing with Molecular Dynamics.        

 Before the B-SURF program I had no idea that computational chemistry even existed. After reading through some papers and meeting with Dr. Reker and my mentor Zilu, I’ve learned that computational chemistry could revolutionize the field of drug development. Through simulating interactions of molecules with the Molecular Dynamics software, we’re able to predict what the resulting body would be if we combined the reactants in real life. Specifically, I’m going to spend my Summer researching the potential formation of nanoparticle complexes between different drug and excipient molecules. While most of the chemistry is flying a bit over my head, I hope that as the Summer goes on, and as I finally get around to taking Organic Chemistry, I will understand more about the chemical details of why and how our simulations of molecules form. I’m also excited to learn more about optimizing the parameters of the simulation to perform more accurate predictions. For now though, I’m happy with this past week’s work and my little knowledge in how to generate simple simulations. I might just be a big nerd, but I find it magical that we’re able to take a simple string of letters and pass through a coding pipeline and out comes a visual model of molecules interacting with each other.


     While I don’t get to go to an in-person lab like my fellow B-SURFer’s, I wouldn’t want to change anything about my experience so far. I’m a learn-by-doing kind of guy, and the flexibility of working in a computational lab fits that perfectly. I also know that as time goes on, and as Dr. Reker’s lab gets established in the new engineering building, we’ll eventually get to translate our simulations into real-life. Overall, I’m very excited for what the future holds, and am extremely grateful for Dr. Reker and Zilu for giving me the chance to study underneath them. Here’s to the start of a great summer!

Here is one of my first simulations. In this example, I simulated the interactions between the anti-cancer drug Sorafenib and Cholic Acid. I’m still working on finding the best way to make a movie to upload, so stay tuned for more cool gifs.

 

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